Epigenomics articles within Nature Communications

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  • Article
    | Open Access

    The impact of chromatin structure on gene expression makes it integral to our understanding of developmental and disease processes. Here, the authors introduce a hierarchical hidden Markov model to systematically annotate chromatin states at multiple length scales, and demonstrate its utility for the elucidation of the role of chromatin structure in gene expression.

    • Eugenio Marco
    • , Wouter Meuleman
    •  & Guo-Cheng Yuan

  • Article
    | Open Access

    Diurnal and seasonal rhythms modulate brain function, but we do not know the genomic basis for these rhythms. Here, Limet al. show diurnal and seasonal rhythms of gene expression in the human brain, their relationship to histone acetylation and DNA methylation, and their disruption in Alzheimer’s disease.

    • Andrew S. P. Lim
    • , Hans-Ulrich Klein
    •  & Philip L. De Jager

  • Article
    | Open Access

    DNA methylation is modulated by environmental factors and has a role in many complex diseases. Here, the authors find that methylation at specific DNA sites is associated with all-cause mortality, and a methylation-based risk score may be informative for risk assessment and stratification.

    • Yan Zhang
    • , Rory Wilson
    •  & Hermann Brenner

  • Article
    | Open Access

    Active enhancers are defined by the presence of post-translational modifications of histones. Here, the authors use these marks to identify enhancers recurrently activated in colorectal cancer and find that these enhancers turn on oncogenes and are associated with known risk loci for developing the disease.

    • Andrea J. Cohen
    • , Alina Saiakhova
    •  & Peter C. Scacheri

  • Article
    | Open Access

    The incidence of type 1 diabetes is increasing, potentially implicating non-genetic factors. Here the authors conduct an epigenome-wide association study in disease-discordant twins and find increased DNA methylation variability at genes associated with immune cell metabolism and the cell cycle.

    • Dirk S. Paul
    • , Andrew E. Teschendorff
    •  & R. David Leslie

  • Article
    | Open Access

    Identification of non-coding variants has outstripped our ability to annotate and interpret them. Dickel et al. present a compendium of over 80,000 putative human heart enhancers and demonstrate that two conserved enhancers are required for proper cardiac function in mice.

    • Diane E. Dickel
    • , Iros Barozzi
    •  & Len A. Pennacchio

  • Article
    | Open Access

    Chromatin architecture is a key regulator of transcriptional processes, however current methods to investigate it have technical limitations. Here, the authors describe a novel chromatin capture technique, CATCH, which can be used to identify and characterize complex genomic interaction networks.

    • Ryan J. Bourgo
    • , Hari Singhal
    •  & Geoffrey L. Greene

  • Article
    | Open Access

    Chromosome conformation is a dynamic process, especially in brain. Here, Mitchell and colleagues devise a method they call NeuroDam that can prospectively tag chromosome conformation in the mouse brain in vivo, and longitudinally assess long range chromosome looping weeks and months later.

    • Amanda C. Mitchell
    • , Behnam Javidfar
    •  & Schahram Akbarian

  • Article
    | Open Access

    Chronic lymphocytic leukemia (CLL) is characterized by substantial clinical heterogeneity. Here, the authors report the genome-wide chromatin accessibility maps for 88 CLL samples from 55 patients using ATAC-seq, and 10 matched RNA-seq datasets, providing a resource for studying epigenome deregulation in CLL.

    • André F. Rendeiro
    • , Christian Schmidl
    •  & Christoph Bock

  • Article
    | Open Access

    Differential impact of genetic and environmental influences on DNA methylation may result in sex- and age-related physiological variation and disease susceptibility. By analysing DNA methylome of 2,603 individuals from twin families, here, the authors establish a catalogue of between-individual variation in DNA methylation.

    • Jenny van Dongen
    • , Michel G. Nivard
    •  & Dorret I. Boomsma

  • Article
    | Open Access

    The human genome is highly organized, with one-dimensional chromatin states packaged into higher level three-dimensional architecture. Here, the authors present EpiTensor that can identify 3D spatial associations from 1D epigenetic information.

    • Yun Zhu
    • , Zhao Chen
    •  & Wei Wang

  • Article
    | Open Access

    Genetic and environmental factors affect genome-wide patterns of epigenetic variation. Here, the authors show that while current habitat and historical lifestyle impact the methylome of rainforest hunter-gatherers and sedentary farmers, the biological functions affected and the degree of genetic control differ.

    • Maud Fagny
    • , Etienne Patin
    •  & Lluis Quintana-Murci

  • Article |

    Characterizing mammalian gene expression regulation by enhancer elements is complicated by the size and complexity of the genome. Here Vanhille et al.demonstrate CapStarr-Seq, a novel high-throughput method for assessing potential enhancers and deciphering the mechanisms regulating transcription

    • Laurent Vanhille
    • , Aurélien Griffon
    •  & Salvatore Spicuglia

  • Article
    | Open Access

    Suppression of MutS HOMOLOGUE 1 (MSH1), a plant protein targeted to mitochondria and plastids, causes a variety of phenotypes. Here Virdi et al. show that MSH1 depletion in Arabidopsisresults in heritable changes in nuclear DNA methylation, which can lead to enhanced growth vigour.

    • Kamaldeep S. Virdi
    • , John D. Laurie
    •  & Sally A. Mackenzie

  • Article
    | Open Access

    Epigenetic changes associated with post-natal differentiation have been characterized. Here the authors generate epigenomic and transcriptional profiles from primary human breast cells, providing insights into the transcriptional and epigenetic events that define post-natal cell differentiation in vivo.

    • Philippe Gascard
    • , Misha Bilenky
    •  & Martin Hirst

  • Article |

    Epigenomes are thought to retain molecular memories of their developmental history. Here, by comparing differentially methylated regions of genomes from different cells, the authors reveal an epigenetic signature that underlies a shared gene regulatory network with a common developmental origin.

    • Rebecca F. Lowdon
    • , Bo Zhang
    •  & Jeffrey B. Cheng

  • Article |

    Pronucleus DNA becomes demethylated during zygotic development. Here, the authors demonstrate that the reduction in 5-methylcytosine levels is accompanied by an increase in the presence of 5-hydroxymethylcytosine, and suggest that this has a role in developmental reprogramming.

    • Mark Wossidlo
    • , Toshinobu Nakamura
    •  & Jörn Walter

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